Demultiplex Illumina BCL files
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
samplesheet
:file
Input samplesheet
*.{csv}
run_dir
Input run directory containing RunInfo.xml and BCL data Could be a directory or a tar of the directory
fastq
Groovy Map containing sample information
output/**_S[1-9]*_R?_00?.fastq.gz
Demultiplexed sample FASTQ files
**_S*_L00?_R?_00?.fastq.gz
fastq_idx
output/**_S[1-9]*_I?_00?.fastq.gz
Optional demultiplexed index FASTQ files
**_S*_L00?_I?_00?.fastq.gz
undetermined
output/**Undetermined_S0*_R?_00?.fastq.gz
Optional undetermined sample FASTQ files
Undetermined_S0_L00?_R?_00?.fastq.gz
undetermined_idx
output/**Undetermined_S0*_I?_00?.fastq.gz
Optional undetermined index FASTQ files
Undetermined_S0_L00?_I?_00?.fastq.gz
reports
output/Reports
Demultiplexing Reports
Reports/*
stats
output/Stats
Statistics files
Stats/*
interop
InterOp/*.bin
Interop files
*.{bin}
versions
versions.yml
File containing software versions
